tbuckley/cabot-search huggingface dataset:
Building Phylogenetic Trees From Genome Sequences With kSNP4
Authors: Barry G Hall, Jeremiah Nisbet
Journal: Molecular Biology and Evolution (2023)

Performing phylogenetic analysis with genome sequences maximizes the information used to estimate phylogenies and the resolution of closely related taxa. The use of single-nucleotide polymorphisms (SNPs) permits estimating trees without genome alignments and permits the use of data sets of hundreds of microbial genomes. kSNP4 is a program that identifies SNPs without using a reference genome, estimates parsimony, maximum likelihood, and neighbor-joining trees, and is able to annotate the discovered SNPs. kSNP4 is a command-line program that does not require any additional programs or dependencies to install or use. kSNP4 does not require any programming experience or bioinformatics experience to install and use. It is suitable for use by students through senior investigators. It includes a detailed user guide that explains all of the many features of kSNP4. In this study, we provide a detailed step-by-step protocol for downloading, installing, and using kSNP4 to build phylogenetic trees from genome sequences.
JAAD Case Reports Article List
Authors: Eloy Ordaya, Daniel Ries, Nikifor Konstantinov, Sahana Ummadi, Shelley Stepenaskie, Sharon Nunez, David Cao, Jessica Zhou, Carl Dernell, Keri Chaney, Karolyn Wanat, Madiha Khan-Walton, Katerina Warda, Sarah Do, Aurel Do, Cindy Apple, Charles Hoffman, Pooja Gropper, Paul Srivastava, Christopher Fay, Jacqueline Lippert, Nicole Leboeuf, Drew Kuraitis, Susan Pei, Doniya Milani, Katharine Hanlon, Lilia Correa-Selm, James Grichnik, Wei-Shen Chen, Christopher Iriarte, Dorsa Moslehi, Jimmy Lam, Igor Katsyv, Kevin Burningham, Ravi Patel, Cristian Gonzalez, Melissa Mauskar, Travis Vandergriff, Heather Goff, William Lau, Yasin Damji, Gregory Orlowski, Elizabeth Jones, Alexander Valiga, Miriam Solowey, Gabriella Alvarez, Larissa Rodriguez-Homs, Rami Al-Rohil, Meenal Kheterpal, Amber Fresco, Katie Roster, Rebecca Kann, Alina Zufall, Banu Farabi, Marian Russo, Kenneth Shulman, Bijan Safai, Patrick Mcmullan, Regina Brown, Lorin Bibb, Katalin Ferenczi, Christina Huang, Adar Berghoff, Jack Arbiser, Michael Woodbury, Rebecca Gaffney, Joseph Merola, Jamie Lebhar, Jennifer Jacobs, Khushnood Faraz, April Salama, Paul Mosca, Karissa Libson, Kristin Koenig, Catherine Chung, Abraham Korman, Zoha Momin, Swapneel Patel, Katherine Gordon, Tatiana Barrera, Omar Venegas, Tiaranesha Jackson, Yacine Sow, Christopher Wachuku, Rosalie Elenitsas, Susan Taylor, Nicholas Mollanazar, Patricia Zhao, Tappy Gish, Diana Mannschreck, Enrica Marchi, Thomas Cropley, Ryan Saal, Luis Borda, Melissa Hoffman, Alice Roberts, Abby Van Voorhees, Jimena Miranda, Charles Huvet, Marie Donzel, Anne Lazareth, Jimmy Perrot, Ste Eng, Fibrofolliculomas In Birt-Hogg-Dubé ´phane Dalle, Rishi Patel, Jesse Wesenberg, Jennifer Brammeier, Aryan Naik, Mihir Patil, Alireza Sepehr, Peter Schalock, Beth Gardner, Thanh-Nga Tran, Roy Jiang, Jonathan Leventhal, Kathleen Suozzi, Taylor Harp, Martin Zaiac, Matthew Kauffman, Taraneh Matin, Jordan Do, Emily Rosen, Angela Moore, Kara Hurley, Stephen Moore, Luke Moore, Faraz Yousefian, Zeynep Deligonul, Lisa Swanson
Journal: Journal of the American Academy of Dermatology (2023)
Emergence of bedaquiline-resistant tuberculosis and of multidrug-resistant and extensively drug-resistant Mycobacterium tuberculosis strains with rpoB Ile491Phe mutation not detected by Xpert MTB/RIF in Mozambique: a retrospective observational study
Authors: Ivan Barilar, Tatiana Fernando, Christian Utpatel, Cláudio Abujate, Carla Maria Madeira, Benedita José, Claudia Mutaquiha, Katharina Kranzer, Tanja Niemann, Nalia Ismael, Leonardo de Araujo, Thierry Wirth, Stefan Niemann, Sofia Viegas
Journal: The Lancet Infectious Diseases (2023)
Geriatric assessment and management: is decreasing treatment toxicity good enough?
Authors: Kah Poh Loh, Supriya G Mohile
Journal: JNCI Journal of the National Cancer Institute (2023)

The majority of new cancer cases occur in older adults.Geriatric assessment and management (or comprehensive geriatric assessment) refers to the use of various validated tools to assess an older adult's health status and guides subsequent therapeutic and supportive care interventions.It is important to note that there are 2 steps to geriatric assessment and management: the evaluation of an older adult's aging-related health conditions (ie, physical performance, cognition) and management through adjusting cancer plan in response to knowledge about aging-related conditions and/or implementing aging-sensitive interventions to address aging-related conditions (eg, physical therapy referral for falls and balance issues), which is recommended by several professional organizations including the American Society of Clinical Oncology, National Comprehensive Cancer Network, and International Society of Geriatric Oncology (1-3).Earlier studies demonstrated that aging-related vulnerabilities uncovered on geriatric assessment are associated with higher morbidity and mortality (4,5), and geriatric assessment measures can predict treatment toxicity (6,7).However, earlier guidelines were not able to establish a defined role for geriatric assessment and management because of a limited number of large, well-designed randomized controlled trials (RCTs).Since 2020, several clinical trials have been conducted to assess the effects of geriatric assessment and management, and a number of systematic reviews have been performed (8)(9)(10)(11).Only one was a meta-analysis by Chuang et al. ( 12) focusing on treatment toxicity, and none included cost-effectiveness data.In this issue, Anwar et al. ( 13) extended the literature by performing a systematic review and meta-analysis on the effectiveness of comprehensive geriatric assessment among older adults receiving curative or palliative treatments.It included 17 RCTs that studied the following outcomes: mortality, hospitalization, readmission, treatment toxicity, change in treatment, quality of life, functional status, and cost (13).Of note, trials were included if geriatric assessment was done and recommendations were provided with or without subsequent implementation.Models of care varied, for instance, centralizations where comprehensive geriatric assessment was performed by a geriatrician, a geriatric oncologist, a trained nurse, or a multidisciplinary geriatric team vs decentralization where comprehensive geriatric assessment was performed by research personnel using validated tools and criteria, results of which were then provided to the treating oncology
Facultative lifestyle drives diversity of coral algal symbionts
Authors: Debashish Bhattacharya, Timothy G. Stephens, Erin E. Chille, L. Felipe Benites, Cheong Xin Chan
Journal: Trends in Ecology & Evolution (2023)

The photosynthetic symbionts of corals sustain biodiverse reefs in nutrient-poor, tropical waters. Recent genomic data illuminate the evolution of coral symbionts under genome size constraints and suggest that retention of the facultative lifestyle, widespread among these algae, confers a selective advantage when compared with a strict symbiotic existence. We posit that the coral symbiosis is analogous to a 'bioreactor' that selects winner genotypes and allows them to rise to high numbers in a sheltered habitat prior to release by the coral host. Our observations lead to a novel hypothesis, the 'stepping-stone model', which predicts that local adaptation under both the symbiotic and free-living stages, in a stepwise fashion, accelerates coral alga diversity and the origin of endemic strains and species.
Opportunities and tradeoffs in single-cell transcriptomic technologies
Authors: Matilde I. Conte, Azahara Fuentes-Trillo, Cecilia Domínguez Conde
Journal: Trends in Genetics (2023)

Recent technological and algorithmic advances enable single-cell transcriptomic analysis with remarkable depth and breadth. Nonetheless, a persistent challenge is the compromise between the ability to profile high numbers of cells and the achievement of full-length transcript coverage. Currently, the field is progressing and developing new and creative solutions that improve cellular throughput, gene detection sensitivity and full-length transcript capture. Furthermore, long-read sequencing approaches for single-cell transcripts are breaking frontiers that have previously blocked full transcriptome characterization. We here present a comprehensive overview of available options for single-cell transcriptome profiling, highlighting the key advantages and disadvantages of each approach.
Host Response Changes and Their Association with Mortality in COVID-19 Patients with Lymphopenia
Authors: Erik H. A. Michels, Brent Appelman, Justin de Brabander, Rombout B. E. van Amstel, Christine C. A. van Linge, Osoul Chouchane, Tom D. Y. Reijnders, Alex R. Schuurman, Titia A. L. Sulzer, Augustijn M. Klarenbeek, Renée A. Douma, Lieuwe D. J. Bos, W. Joost Wiersinga, Hessel Peters-Sengers, Tom van der Poll, Michiel van Agtmael, Anne Geke Algera, Brent Appelman, Floor van Baarle, Martijn Beudel, Harm Jan Bogaard, Marije Bomers Peter Bonta, Lieuwe Bos, Michela Botta, Justin de Brabander, Godelieve de Bree, Sanne de Bruin, Marianna Bugiani, Esther Bulle, David T. P. Buis, Osoul Chouchane Alex Cloherty, Mirjam Dijkstra, Dave A. Dongelmans, Romein W. G. Dujardin, Paul Elbers, Lucas Fleuren, Suzanne Geerlings Theo Geijtenbeek, Armand Girbes, Bram Goorhuis, Martin P. Grobusch, Laura Hagens, Jorg Hamann, Vanessa Harris, Robert Hemke, Sabine M. Hermans Leo Heunks, Markus Hollmann, Janneke Horn, Joppe W. Hovius, Hanna K. de Jong, Menno D. de Jong, Rutger Koning, Bregje Lemkes, Endry H. T. Lim, Niels van Mourik, Jeaninne Nellen, Esther J. Nossent, Sabine Olie, Frederique Paulus, Edgar Peters, Dan A. I. Pina-Fuentes, Tom van der Poll, Bennedikt Preckel, Jorinde Raasveld, Tom Reijnders, Maurits C. F. J. de Rotte, Michiel Schinkel, Marcus J. Schultz, Femke A. P. Schrauwen, Alex Schuurman, Jaap Schuurmans, Kim Sigaloff, Marleen A. Slim, Patrick Smeele, Marry Smit, Cornelis S. Stijnis, Willemke Stilma, Charlotte Teunissen, Patrick Thoral, Anissa M. Tsonas, Pieter R. Tuinman, Marc van der Valk, Denise P. Veelo, Carolien Volleman, Heder de Vries, Lonneke A. Vught, Michèle van Vugt, Dorien Wouters, A. H. (Koos) Zwinderman, Matthijs C. Brouwer, W. Joost Wiersinga, Alexander P. J. Vlaar, Diederik van de Beek
Journal: American Journal of Respiratory and Critical Care Medicine (2023)

Lymphopenia in coronavirus disease (COVID-19) is associated with increased mortality.
Transcriptomes and metabolism define mouse and human MAIT cell populations
Authors: Shilpi Chandra, Gabriel Ascui, Thomas Riffelmacher, Ashu Chawla, Ciro Ramírez-Suástegui, Viankail C. Castelan, Gregory Seumois, Hayley Simon, Mallory P. Murray, Goo-Young Seo, Ashmitaa L. R. Premlal, Benjamin Schmiedel, Greet Verstichel, Yingcong Li, Chia-Hao Lin, Jason Greenbaum, John Lamberti, Raghav Murthy, John Nigro, Hilde Cheroutre, Christian H. Ottensmeier, Stephen M. Hedrick, Li-Fan Lu, Pandurangan Vijayanand, Mitchell Kronenberg
Journal: Science Immunology (2023)

Mucosal-associated invariant T (MAIT) cells are a subset of T lymphocytes that respond to microbial metabolites. We defined MAIT cell populations in different organs and characterized the developmental pathway of mouse and human MAIT cells in the thymus using single-cell RNA sequencing and phenotypic and metabolic analyses. We showed that the predominant mouse subset, which produced IL-17 (MAIT17), and the subset that produced IFN-γ (MAIT1) had not only greatly different transcriptomes but also different metabolic states. MAIT17 cells in different organs exhibited increased lipid uptake, lipid storage, and mitochondrial potential compared with MAIT1 cells. All these properties were similar in the thymus and likely acquired there. Human MAIT cells in lung and blood were more homogeneous but still differed between tissues. Human MAIT cells had increased fatty acid uptake and lipid storage in blood and lung, similar to human CD8 T resident memory cells, but unlike mouse MAIT17 cells, they lacked increased mitochondrial potential. Although mouse and human MAIT cell transcriptomes showed similarities for immature cells in the thymus, they diverged more strikingly in the periphery. Analysis of pet store mice demonstrated decreased lung MAIT17 cells in these so-called "dirty" mice, indicative of an environmental influence on MAIT cell subsets and function.
Simple model systems reveal conserved mechanisms of Alzheimer’s disease and related tauopathies
Authors: Yuwei Jiang, Lesley T MacNeil
Journal: Molecular Neurodegeneration (2023)

The lack of effective therapies that slow the progression of Alzheimer's disease (AD) and related tauopathies highlights the need for a more comprehensive understanding of the fundamental cellular mechanisms underlying these diseases. Model organisms, including yeast, worms, and flies, provide simple systems with which to investigate the mechanisms of disease. The evolutionary conservation of cellular pathways regulating proteostasis and stress response in these organisms facilitates the study of genetic factors that contribute to, or protect against, neurodegeneration. Here, we review genetic modifiers of neurodegeneration and related cellular pathways identified in the budding yeast Saccharomyces cerevisiae, the nematode Caenorhabditis elegans, and the fruit fly Drosophila melanogaster, focusing on models of AD and related tauopathies. We further address the potential of simple model systems to better understand the fundamental mechanisms that lead to AD and other neurodegenerative disorders.
Zfp281 and Zfp148 control CD4 <sup>+</sup> T cell thymic development and T <sub>H</sub> 2 functions
Authors: Laura B. Chopp, Xiaoliang Zhu, Yayi Gao, Jia Nie, Jatinder Singh, Parimal Kumar, Kelly Z. Young, Shil Patel, Caiyi Li, Mariah Balmaceno-Criss, Melanie S. Vacchio, Michael M. Wang, Ferenc Livak, Juanita L. Merchant, Lie Wang, Michael C. Kelly, Jinfang Zhu, Rémy Bosselut
Journal: Science Immunology (2023)

How CD4+ lineage gene expression is initiated in differentiating thymocytes remains poorly understood. Here, we show that the paralog transcription factors Zfp281 and Zfp148 control both this process and cytokine expression by T helper cell type 2 (TH2) effector cells. Genetic, single-cell, and spatial transcriptomic analyses showed that these factors promote the intrathymic CD4+ T cell differentiation of class II major histocompatibility complex (MHC II)-restricted thymocytes, including expression of the CD4+ lineage-committing factor Thpok. In peripheral T cells, Zfp281 and Zfp148 promoted chromatin opening at and expression of TH2 cytokine genes but not of the TH2 lineage-determining transcription factor Gata3. We found that Zfp281 interacts with Gata3 and is recruited to Gata3 genomic binding sites at loci encoding Thpok and TH2 cytokines. Thus, Zfp148 and Zfp281 collaborate with Gata3 to promote CD4+ T cell development and TH2 cell responses.
Metformin-Cimetidine Drug Interaction and Risk of Lactic Acidosis in Renal Failure: A Pharmacovigilance-Pharmacokinetic Appraisal
Authors: Wenhuo Xie, Jianbin Li, Chenghua Kong, Wei Luo, Jiaping Zheng, Yu Zhou
Journal: Diabetes Care (2023)

This study aimed to evaluate lactic acidosis (LA) risk when using metformin combined with histamine H2 receptor inhibitors (H2RI) in patients with renal failure (RF).This study analyzed FDA Adverse Event Reporting System data (2012Q4 to 2022Q4) to characterize reports of LA associated with metformin alone or combined with H2RI. Using a disproportionality approach, LA risk signal in the overall population and in patients with RF was assessed. A physiologically based pharmacokinetic (PBPK) model was developed to predict metformin and cimetidine pharmacokinetic changes following conventional doses of the combinations in patients with various degrees of RF. To explore its correlation with LA risk, a peak plasma metformin concentration of 3 mg/L was considered the threshold.Following the 2016 U.S. Food and Drug Administration metformin approval for mild-to-moderate RF, the percentage of patients with RF reporting LA associated with metformin combined with H2RI increased. Disproportionality analysis showed reported LA risk signal associated with metformin and cimetidine in the overall population within the study timeframe only. Furthermore, with PBPK simulations, for metformin (1,000 mg b.i.d.) with cimetidine (300 mg q.i.d. or 400 mg b.i.d.) in stage 1 of chronic kidney disease, metformin (1,000 mg b.i.d.) with cimetidine (300 mg q.i.d. or 400 mg b.i.d. or 800 mg q.d.) in stage 2, and most combinations in stage 3, the peak plasma metformin concentrations exceeded the 3 mg/L threshold.Metformin combined with cimetidine at conventional doses may cause LA in patients with mild-to-moderate RF.
Automatic registration with continuous pose updates for marker-less surgical navigation in spine surgery
Authors: Florentin Liebmann, Marco von Atzigen, Dominik Stütz, Julian Wolf, Lukas Zingg, Daniel Suter, Nicola A. Cavalcanti, Laura Leoty, Hooman Esfandiari, Jess G. Snedeker, Martin R. Oswald, Marc Pollefeys, Mazda Farshad, Philipp Fürnstahl
Journal: Medical Image Analysis (2023)

Established surgical navigation systems for pedicle screw placement have been proven to be accurate, but still reveal limitations in registration or surgical guidance. Registration of preoperative data to the intraoperative anatomy remains a time-consuming, error-prone task that includes exposure to harmful radiation. Surgical guidance through conventional displays has well-known drawbacks, as information cannot be presented in-situ and from the surgeon's perspective. Consequently, radiation-free and more automatic registration methods with subsequent surgeon-centric navigation feedback are desirable. In this work, we present a marker-less approach that automatically solves the registration problem for lumbar spinal fusion surgery in a radiation-free manner. A deep neural network was trained to segment the lumbar spine and simultaneously predict its orientation, yielding an initial pose for preoperative models, which then is refined for each vertebra individually and updated in real-time with GPU acceleration while handling surgeon occlusions. An intuitive surgical guidance is provided thanks to the integration into an augmented reality based navigation system. The registration method was verified on a public dataset with a median of 100% successful registrations, a median target registration error of 2.7 mm, a median screw trajectory error of 1.6°and a median screw entry point error of 2.3 mm. Additionally, the whole pipeline was validated in an ex-vivo surgery, yielding a 100% screw accuracy and a median target registration error of 1.0 mm. Our results meet clinical demands and emphasize the potential of RGB-D data for fully automatic registration approaches in combination with augmented reality guidance.
Sprayable Multifunctional Black Phosphorus Hydrogel with On‐Demand Removability for Joint Skin Wound Healing
Authors: Xiaoya Ding, Yunru Yu, Lu Fan, Wenzhao Li, Feika Bian, Jinglin Wang, Yuanjin Zhao
Journal: Advanced Healthcare Materials (2023)

Abstract Wound healing remains a critical challenge in regenerative engineering. Great efforts are devoted to develop functional patches for wound healing. Herein, a novel sprayable black phosphorus (BP)‐based multifunctional hydrogel with on‐demand removability is presented as a joints’ skin wound dressing. The hydrogel is facilely prepared by mixing dopamine‐modified oxidized hyaluronic acid, cyanoacetategroup‐functionalized dextran containing black phosphorus, and the catalyst histidine. The catechol‐containing dopamine can not only enhance tissue adhesiveness, but also endow the hydrogel with antioxidant capacity. In addition, benefiting from the photothermal conversion ability of the BP and thermally reversible performance of the formed C═C double bonds between aldehyde groups and cyanoacetate groups, the resulting hydrogel displays excellent antibacterial performance and on‐demand dissolving ability under NIR irradiation. Moreover, by loading vascular endothelial growth factor into the hydrogel, the promoted migration and angiogenesis effects of endothelial cells can also be achieved. Based on these features, it is demonstrated that such sprayable BP hydrogels can effectively facilitate joint wounds healing by accelerating angiogenesis, alleviating inflammation, and improving wound microenvironment. Thus, it is believed that this NIR‐responsive removable BP hydrogel dressing will put forward an innovative concept in designing wound dressings.
A Multicenter Prospective Evaluation of the Benefits of Two Advanced Hybrid Closed-Loop Systems in Glucose Control and Patient-Reported Outcomes in a Real-world Setting
Authors: Pilar Isabel Beato-Víbora, Ana Chico, Jesus Moreno-Fernandez, Virginia Bellido-Castañeda, Lia Nattero-Chávez, María José Picón-César, María Asunción Martínez-Brocca, Marga Giménez-Álvarez, Eva Aguilera-Hurtado, Elisenda Climent-Biescas, Sharona Azriel-Mir, Ángel Rebollo-Román, Carmen Yoldi-Vergara, Marcos Pazos-Couselo, Nuria Alonso-Carril, Carmen Quirós
Journal: Diabetes Care (2023)

OBJECTIVE Advanced hybrid closed-loop systems (AHCL) have been shown to improve glycemic control and patient-reported outcomes in type 1 diabetes. The aim was to analyze the outcomes of two commercially available AHCL in real life. RESEARCH DESIGN AND METHODS A prospective study was performed, including adolescents and adults with type 1 diabetes, AHCL naïve, from 14 centers, who initiated the use of MM780G with SmartGuard or Tandem t:slimX2 with Control-IQ. Baseline and 3-month evaluations were performed, assessing HbA1c, time in different glycemic ranges, and patient-reported outcomes. The primary outcome was the between-group time in range 70–180 mg/dL difference from beginning to end of follow-up. RESULTS One hundred fifty participants were included, with 75 initiating each system (age: 39.9 ± 11.4 years [16–72]; 64% female; diabetes duration: 21.6 ± 11.9 years). Time in range increased from 61.53 ± 14.01% to 76.17 ± 9.48% (P &amp;lt; 0.001), with no between-group differences (P = 0.591). HbA1c decreased by 0.56% (95% CI 0.44%, 0.68%) (6 mmol/mol, 95% CI 5, 7) (P &amp;lt; 0.001), from 7.43 ± 1.07% to 6.88 ± 0.60% (58 ± 12 to 52 ± 7 mmol/mol) in the MM780G group, and from 7.14 ± 0.70% to 6.56 ± 0.53% (55 ± 8 to 48 ± 6 mmol/mol) in the Control-IQ group (both P &amp;lt; 0.001 to baseline, P = 0.819 between groups). No superiority of one AHCL over the other regarding fear of hypoglycemia or quality of life was found. Improvement in diabetes-related distress was higher in Control-IQ users (P = 0.012). Sleep quality was improved (PSQI: from 6.94 ± 4.06 to 6.06 ± 4.05, P = 0.004), without differences between systems. Experience with AHCL, evaluated by the INSPIRE measures, exceeded the expectations. CONCLUSIONS The two AHCL provide significant improvement in glucose control and satisfaction, with no superiority of one AHCL over the other.
A hidden pandemic: the danger of donated respiratory devices to children in LMICs
Authors: Nadia E Hoekstra, Bryan Vonasek, Tisungane Mvalo, Yewo Nyondo, Eric D McCollum
Journal: The Lancet Global Health (2023)

During the COVID-19 pandemic, a home ventilator was donated to a tertiary-care hospital in Malawi to support adults with respiratory failure. As the pandemic waned, this ventilator was reallocated to the paediatric ward and, in an effort to help a girl aged 8 years with life-threatening pneumonia, paediatric staff used the ventilator with a mask. The staff were untrained on the ventilator and confused it with a continuous positive airway pressure machine, resulting in inadvertent use of volume-targeted pressure support.